Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/progs/ztr_dump.c @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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rev | line source |
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0
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 #include <stdio.h> |
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2 #include <errno.h> |
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3 #include <math.h> |
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4 #include <io_lib/ztr.h> |
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5 #include <io_lib/compression.h> |
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6 #include <io_lib/xalloc.h> |
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7 |
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8 static char *format2str(int format) { |
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9 static char unk[100]; |
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10 |
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11 switch (format) { |
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12 case ZTR_FORM_RAW: return "raw"; |
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13 case ZTR_FORM_RLE: return "rle"; |
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14 case ZTR_FORM_XRLE: return "xrle"; |
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15 case ZTR_FORM_XRLE2: return "xrle2"; |
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16 case ZTR_FORM_ZLIB: return "zlib"; |
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17 case ZTR_FORM_DELTA1: return "delta1"; |
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18 case ZTR_FORM_DELTA2: return "delta2"; |
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19 case ZTR_FORM_DELTA4: return "delta4"; |
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20 case ZTR_FORM_DDELTA1: return "ddelta1"; |
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21 case ZTR_FORM_DDELTA2: return "ddelta2"; |
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22 case ZTR_FORM_DDELTA4: return "ddelta4"; |
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23 case ZTR_FORM_16TO8: return "16to8"; |
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24 case ZTR_FORM_32TO8: return "32to8"; |
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25 case ZTR_FORM_FOLLOW1: return "follow1"; |
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26 case ZTR_FORM_CHEB445: return "cheb445"; |
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27 case ZTR_FORM_ICHEB: return "icheb"; |
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28 case ZTR_FORM_LOG2: return "log2"; |
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29 case ZTR_FORM_STHUFF: return "sthuff"; |
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30 case ZTR_FORM_QSHIFT: return "qshift"; |
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31 case ZTR_FORM_TSHIFT: return "tshift"; |
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32 } |
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33 |
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34 sprintf(unk, "?%d?\n", format); |
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35 return unk; |
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36 } |
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37 |
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38 /* |
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39 * Shannon showed that for storage in base 'b' with alphabet symbols 'a' having |
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40 * a probability of ocurring in any context of 'Pa' we should encode |
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41 * symbol 'a' to have a storage width of -logb(Pa). |
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42 * |
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43 * Eg. b = 26, P(e) = .22. => width .4647277. |
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44 * |
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45 * We use this to calculate the entropy of a signal by summing over all letters |
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46 * in the signal. In this case, our storage has base 256. |
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47 */ |
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48 #define EBASE 256 |
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49 double entropy(unsigned char *data, int len) { |
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50 double E[EBASE]; |
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51 double P[EBASE]; |
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52 double e; |
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53 int i; |
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54 |
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55 for (i = 0; i < EBASE; i++) |
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56 P[i] = 0; |
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57 |
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58 for (i = 0; i < len; i++) |
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59 P[data[i]]++; |
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60 |
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61 for (i = 0; i < EBASE; i++) { |
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62 if (P[i]) { |
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63 P[i] /= len; |
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64 E[i] = -(log(P[i])/log(EBASE)); |
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65 } else { |
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66 E[i] = 0; |
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67 } |
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68 } |
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69 |
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70 for (e = i = 0; i < len; i++) |
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71 e += E[data[i]]; |
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72 |
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73 return e; |
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74 } |
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75 |
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76 /* Debug version of the ztr.c uncompress_chunk function. */ |
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77 static int explode_chunk(ztr_t *ztr, ztr_chunk_t *chunk) { |
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78 char *new_data = NULL; |
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79 int new_len; |
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80 |
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81 while (chunk->dlength > 0 && chunk->data[0] != ZTR_FORM_RAW) { |
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82 double ent = entropy((unsigned char *)chunk->data, chunk->dlength); |
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83 |
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84 switch (chunk->data[0]) { |
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85 case ZTR_FORM_RLE: |
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86 new_data = unrle(chunk->data, chunk->dlength, &new_len); |
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87 break; |
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88 |
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89 case ZTR_FORM_XRLE: |
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90 new_data = unxrle(chunk->data, chunk->dlength, &new_len); |
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91 break; |
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92 |
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93 case ZTR_FORM_XRLE2: |
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94 new_data = unxrle2(chunk->data, chunk->dlength, &new_len); |
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95 break; |
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96 |
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97 case ZTR_FORM_ZLIB: |
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98 new_data = zlib_dehuff(chunk->data, chunk->dlength, &new_len); |
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99 break; |
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100 |
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101 case ZTR_FORM_DELTA1: |
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102 new_data = recorrelate1(chunk->data, chunk->dlength, &new_len); |
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103 break; |
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104 |
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105 case ZTR_FORM_DELTA2: |
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106 new_data = recorrelate2(chunk->data, chunk->dlength, &new_len); |
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107 break; |
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108 |
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109 case ZTR_FORM_DELTA4: |
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110 new_data = recorrelate4(chunk->data, chunk->dlength, &new_len); |
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111 break; |
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112 |
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113 case ZTR_FORM_16TO8: |
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114 new_data = expand_8to16(chunk->data, chunk->dlength, &new_len); |
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115 break; |
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116 |
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117 case ZTR_FORM_32TO8: |
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118 new_data = expand_8to32(chunk->data, chunk->dlength, &new_len); |
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119 break; |
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120 |
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121 case ZTR_FORM_FOLLOW1: |
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122 new_data = unfollow1(chunk->data, chunk->dlength, &new_len); |
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123 break; |
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124 |
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125 case ZTR_FORM_ICHEB: |
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126 new_data = ichebuncomp(chunk->data, chunk->dlength, &new_len); |
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127 break; |
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128 |
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129 case ZTR_FORM_LOG2: |
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130 new_data = unlog2_data(chunk->data, chunk->dlength, &new_len); |
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131 break; |
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132 |
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133 case ZTR_FORM_STHUFF: |
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134 new_data = unsthuff(ztr, chunk->data, chunk->dlength, &new_len); |
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135 break; |
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136 |
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137 case ZTR_FORM_QSHIFT: |
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138 new_data = unqshift(chunk->data, chunk->dlength, &new_len); |
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139 break; |
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140 |
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141 case ZTR_FORM_TSHIFT: |
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142 new_data = untshift(ztr, chunk->data, chunk->dlength, &new_len); |
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143 break; |
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144 |
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145 default: |
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146 fprintf(stderr, "Unknown encoding format %d\n", chunk->data[0]); |
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147 return -1; |
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148 } |
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149 |
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150 if (!new_data) { |
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151 fprintf(stderr, "Failed to decode chunk with format %s\n", |
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152 format2str(chunk->data[0])); |
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153 return -1; |
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154 } |
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155 |
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156 printf(" format %8s => %6d to %6d, entropy %8.1f to %8.1f\n", |
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157 format2str(chunk->data[0]), chunk->dlength, new_len, |
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158 ent, entropy((unsigned char *)new_data, new_len)); |
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159 |
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160 chunk->dlength = new_len; |
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161 xfree(chunk->data); |
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162 chunk->data = new_data; |
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163 } |
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164 |
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165 return 0; |
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166 } |
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167 |
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168 int main(int argc, char **argv) { |
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169 ztr_t *ztr; |
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170 mFILE *fp; |
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171 int i; |
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172 |
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173 if (argc >= 2) { |
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174 if (NULL == (fp = mfopen(argv[1], "rb"))) { |
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175 perror(argv[1]); |
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176 return 1; |
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177 } |
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178 } else { |
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179 fp = mstdin(); |
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180 } |
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181 |
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182 if (NULL == (ztr = mfread_ztr(fp))) { |
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183 perror("fread_ztr"); |
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184 return 1; |
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185 } |
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186 |
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187 printf("Nchunks = %d\n", ztr->nchunks); |
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188 for (i = 0; i < ztr->nchunks; i++) { |
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189 char str[5]; |
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190 int complen; |
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191 int rawlen; |
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192 char *val; |
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193 |
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194 (void)ZTR_BE2STR(ztr->chunk[i].type, str); |
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195 complen = ztr->chunk[i].dlength; |
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196 val = ztr_lookup_mdata_value(ztr, &ztr->chunk[i], "TYPE"); |
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197 if (val) |
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198 printf("-- %s (%s) --\n", str, val); |
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199 else |
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200 printf("-- %s --\n", str); |
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201 explode_chunk(ztr, &ztr->chunk[i]); |
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202 rawlen = ztr->chunk[i].dlength; |
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203 printf("SUMMARY %s mlen %3d, dlen %6d, rawlen %6d, ratio %f\n", |
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204 str, ztr->chunk[i].mdlength, |
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205 complen, rawlen, (double)complen/rawlen); |
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206 #if 0 |
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207 fflush(stdout); |
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208 puts("\n========================================"); |
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209 write(1, ztr->chunk[i].data, ztr->chunk[i].dlength); |
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210 puts("\n========================================"); |
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211 #endif |
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212 } |
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213 |
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214 delete_ztr(ztr); |
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215 |
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216 return 0; |
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217 } |